Structure of 53BP1 Tudor domains in complex with small molecule UNC3474

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering.

Cui, G.Botuyan, M.V.Drane, P.Hu, Q.Bragantini, B.Thompson, J.R.Schuller, D.J.Detappe, A.Perfetti, M.T.James, L.I.Frye, S.V.Chowdhury, D.Mer, G.

(2023) Nat Commun 14: 6091-6091

  • DOI: https://doi.org/10.1038/s41467-023-41821-6
  • Primary Citation of Related Structures:  
    6MXX, 6MXY, 6MXZ, 6MY0, 8U4U

  • PubMed Abstract: 

    The recruitment of 53BP1 to chromatin, mediated by its recognition of histone H4 dimethylated at lysine 20 (H4K20me2), is important for DNA double-strand break repair. Using a series of small molecule antagonists, we demonstrate a conformational equilibrium between an open and a pre-existing lowly populated closed state of 53BP1 in which the H4K20me2 binding surface is buried at the interface between two interacting 53BP1 molecules. In cells, these antagonists inhibit the chromatin recruitment of wild type 53BP1, but do not affect 53BP1 variants unable to access the closed conformation despite preservation of the H4K20me2 binding site. Thus, this inhibition operates by shifting the conformational equilibrium toward the closed state. Our work therefore identifies an auto-associated form of 53BP1-autoinhibited for chromatin binding-that can be stabilized by small molecule ligands encapsulated between two 53BP1 protomers. Such ligands are valuable research tools to study the function of 53BP1 and have the potential to facilitate the development of new drugs for cancer therapy.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TP53-binding protein 1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
123Homo sapiensMutation(s): 0 
Gene Names: TP53BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12888 (Homo sapiens)
Explore Q12888 
Go to UniProtKB:  Q12888
PHAROS:  Q12888
GTEx:  ENSG00000067369 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12888
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on K6S

Download Ideal Coordinates CCD File 
K [auth A],
M [auth D],
P [auth E],
T [auth H],
V [auth I]
C17 H28 N2 O
Query on FMT

Download Ideal Coordinates CCD File 
L [auth B]
N [auth D]
O [auth D]
Q [auth F]
R [auth F]
L [auth B],
N [auth D],
O [auth D],
Q [auth F],
R [auth F],
S [auth G],
U [auth H]
C H2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
K6S BindingDB:  6MXZ IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.665α = 90
b = 160.708β = 90
c = 182.647γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA132878

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description